PhD Chapter 1

Campaign 2016 - Maps and exploration

This series of files compile analyses done for the specific analysis of Chapter 1, for the regional campaign of 2016.

All analyses have been done with PRIMER-e 6 and R 4.1.0.

Click on the table of contents in the left margin to assess a specific analysis.
Click on a figure to zoom it

We used data from subtidal ecosystems (see metadata files for more information). Only stations that have been sampled both for abiotic parameters and benthic species were included.

Selected variables for the analyses:

Depth of the station: depth (only for ANCOVAs)
Percentage of organic matter: om
Percentage of gravel: gravel
Percentage of sand: sand
Percentage of silt: silt
Percentage of clay: clay
Concentration of arsenic: arsenic
Concentration of cadmium: cadmium
Concentration of chromium: chromium
Concentration of copper: copper
Concentration of iron: iron
Concentration of manganese: manganese
Concentration of mercury: mercury
Concentration of lead: lead
Concentration of zinc: zinc
Specific richness: S
Total density of individuals: N
Shannon’s diversity: H
Piélou’s evenness: J

Abundances of Mesodesma arctatum (Marc) and Cistenides granulata (Cgra) were also considered (see IndVal and SIMPER results).

As data is missing for metal concentrations outside BSI, two Designs have been used:

Design 1: stations at BSI, CPC, BDA, MR with habitat parameters
Design 2: stations at BSI with heavy metal concentrations.

1. Statistics

Calculation of basic statistics for each variable considered:

	Mean	SD	SE	Median	Min	Max	95% CI
depth	20.235	16.929	2.582	17.600	1.000	65.900	5.060
om	0.856	0.891	0.136	0.491	0.209	3.863	0.266
gravel	0.043	0.092	0.014	0.000	0.000	0.359	0.028
sand	0.612	0.381	0.058	0.702	0.000	1.001	0.114
silt	0.285	0.328	0.050	0.116	0.000	0.942	0.098
clay	0.060	0.106	0.016	0.016	0.000	0.415	0.032
S	4.930	3.135	0.478	4.000	0.000	13.000	0.937
N	18.977	24.421	3.724	12.000	0.000	140.000	7.299
H	1.124	0.613	0.093	1.213	0.000	2.307	0.183
J	0.744	0.291	0.044	0.835	0.000	1.000	0.087
arsenic	4.300	4.759	0.971	2.500	0.800	21.300	1.904
cadmium	0.153	0.048	0.010	0.145	0.080	0.270	0.019
chromium	49.667	24.539	5.009	40.500	17.000	111.000	9.817
copper	9.787	7.764	1.585	7.800	2.400	28.800	3.106
iron	45356.633	17343.813	3540.291	39733.450	21938.100	85408.600	6938.843
manganese	776.662	362.884	74.073	677.850	318.400	1657.100	145.181
mercury	0.023	0.017	0.004	0.019	0.007	0.091	0.007
lead	5.421	3.021	0.617	4.650	1.900	12.200	1.209
zinc	59.358	30.340	6.193	47.700	26.900	141.400	12.138

	Mean	SD	SE	Median	Min	Max	95% CI
depth	20.527	17.297	3.011	15.300	3.400	61.900	5.901
om	0.476	0.389	0.068	0.315	0.168	1.597	0.133
gravel	0.049	0.147	0.026	0.000	0.000	0.809	0.050
sand	0.832	0.270	0.047	0.960	0.000	1.000	0.092
silt	0.095	0.180	0.031	0.023	0.000	0.650	0.061
clay	0.024	0.086	0.015	0.005	0.000	0.497	0.029
S	4.333	2.558	0.445	4.000	1.000	9.000	0.873
N	19.970	27.779	4.836	12.000	2.000	142.000	9.478
H	0.975	0.589	0.102	0.974	0.000	1.985	0.201
J	0.690	0.302	0.053	0.840	0.000	1.000	0.103

2. Maps

2.1. General map

2.2. Parameters maps

For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity (grey = low toxicity, red = high toxicity).

OM

Gravel

Sand

Silt

Clay

Arsenic

Cadmium

Chromium

Copper

Iron

Manganese

Mercury

Lead

Zinc

Species

Richness

Density

Diversity

Evenness

3. Figures

3.1. Barplots

Two types of barplots are available: one for the means by region, and one for the means by depth class. The latter have been done by classifying stations along three groups, based on their depth: shallow (0-10 m), medium (10-25 m) and deep (> 25 m). These thresholds are not supported by evidence, but allow to get a balanced design (26 stations for each depth class). However, we have been using PERMANOVA with depth as a covariate, instead of using these classes as a third factor.

Heavy metals are not presented here, as they were only sampled at BSI stations.

Regions

Organic matter

Grain-size

Species abundances

Diversity indices

Depth classes

Organic matter

Grain-size

Species abundances

Diversity indices

3.2. Phylum frequencies

Conditions

Phylum abundances by condition
Phylum	HI	R
Annelida	275	231
Echinodermata	230	162
Mollusca	196	189
Arthropoda	110	73
Platyhelminthes	3	0
Nematoda	1	0
Nemertea	1	0
Brachiopoda	0	2
Cnidaria	0	2

Regions

Phylum abundances by region
Phylum	BSI	CPC	BDA	MR
Annelida	206	69	188	43
Mollusca	151	45	89	100
Arthropoda	97	13	30	43
Echinodermata	24	206	24	138
Platyhelminthes	3	0	0	0
Nematoda	1	0	0	0
Nemertea	1	0	0	0
Brachiopoda	0	0	0	2
Cnidaria	0	0	0	2